Low-density parity-check (LDPC) codes are among the most prominent error-correction schemes in today’s data-driven world. They find application to fortify various modern storage, communication, and computing systems. Protograph-based (PB) LDPC codes offer many degrees of freedom in the code design and enable fast encoding and decoding. In particular, spatially-coupled (SC) and multi-dimensional (MD) circulant-based codes are PB-LDPC codes with excellent performance. Efficient finite-length (FL) algorithms are required in order to effectively exploit the available degrees of freedom offered by SC partitioning, lifting, and MD relocations. In this paper, we propose a novel Markov chain Monte Carlo (MCMC or MC2) method to perform this FL optimization, addressing the removal of short cycles. While we focus on partitioning and lifting of SC codes, our MC2approach can effectively work for other procedures and/or other code designs. While iterating, we draw samples from a defined distribution where the probability decreases as the number of short cycles from the previous iteration increases. We analyze our MC2method theoretically as we prove the invariance of the Markov chain where each state represents a possible partitioning or lifting arrangement, i.e., sample, that has a specific probability. Via our simulations, we then fit the distribution of the number of cycles resulting from a given arrangement on a Gaussian distribution. By analyzing the mean, we derive estimates for cycle counts that are close to the actual counts. Furthermore, we derive the order of the expected number of iterations required by our MC2approach to reach a local minimum as well as the size of the Markov chain recurrent class through approximating the probability of getting arbitrarily close to the local minimum. Our approach is compatible with code design techniques based on gradient-descent. Experimental results show that our MC2method generates SC codes with remarkably fewer short cycles and substantial gains in error/erasure-rate performance compared with the current state-of-the-art. Moreover, to reach the same number of cycles, our MC2method requires orders of magnitude less overall time compared with the available literature methods.